# -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/stable/config

# -- Path setup --------------------------------------------------------------

# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
from pkg_resources import get_distribution
import os
# import sys
# sys.path.insert(0, os.path.abspath('.'))
# Do not generate APIdocs for members missing docstrings (undoc-members)
os.environ['APIDOC_OPTIONS'] = 'members,show-inheritence,inherited-members'

# Set APIDOC options
#os.environ['SPHINX_APIDOC_OPTIONS'] = 'members,undoc-members,show-inheritance,special-members'
os.environ['SPHINX_APIDOC_OPTIONS'] = 'members'

# -- Project information -----------------------------------------------------

project = 'VerMoUTH'
copyright = '2018, University of Groningen'
author = 'Peter C Kroon, Jonathan Barnoud, Tsjerk A Wassenaar, Siewert-Jan Marrink'

# The full version, including alpha/beta/rc tags
release = get_distribution('vermouth').version
# The short X.Y version
# version = '.'.join(release.split('.')[:2])
version = release

# -- General configuration ---------------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
    'sphinx.ext.autodoc',
    'sphinx.ext.intersphinx',
    'sphinx.ext.mathjax',
    'sphinx.ext.viewcode',
    'sphinx.ext.napoleon',
    'sphinx.ext.autosectionlabel',
    'sphinx.ext.apidoc',
]

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
source_suffix = '.rst'

# The master toctree document.
master_doc = 'index'

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = 'en'

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path .
exclude_patterns = []

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'


nitpick_ignore = [
        ('py:class', 'networkx.algorithms.isomorphism.isomorphvf2.GraphMatcher'),
        ('py:class', 'optional'),
        ]

# -- Options for HTML output -------------------------------------------------

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.
#
html_theme = 'alabaster'

# Theme options are theme-specific and customize the look and feel of a theme
# further.  For a list of options available for each theme, see the
# documentation.
#
# html_theme_options = {}

# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']

# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# The default sidebars (for documents that don't match any pattern) are
# defined by theme itself.  Builtin themes are using these templates by
# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
# 'searchbox.html']``.
#
# html_sidebars = {}


# -- Options for HTMLHelp output ---------------------------------------------

# Output file base name for HTML help builder.
htmlhelp_basename = 'VerMoUTHdoc'


# -- Options for LaTeX output ------------------------------------------------

latex_elements = {
    # The paper size ('letterpaper' or 'a4paper').
    #
    # 'papersize': 'letterpaper',

    # The font size ('10pt', '11pt' or '12pt').
    #
    # 'pointsize': '10pt',

    # Additional stuff for the LaTeX preamble.
    #
    # 'preamble': '',

    # Latex figure (float) alignment
    #
    # 'figure_align': 'htbp',
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
#  author, documentclass [howto, manual, or own class]).
latex_documents = [
    (master_doc, 'VerMoUTH.tex', 'VerMoUTH Documentation',
     author, 'manual'),
]


# -- Options for manual page output ------------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    (master_doc, 'vermouth', 'VerMoUTH Documentation',
     [author], 1)
]


# -- Options for Texinfo output ----------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
#  dir menu entry, description, category)
texinfo_documents = [
    (master_doc, 'VerMoUTH', 'VerMoUTH Documentation',
     author, 'VerMoUTH', 'One line description of project.',
     'Miscellaneous'),
]


# -- Extension configuration -------------------------------------------------
apidoc_modules = [
    {'path': '../../vermouth',
     'destination': 'api',
     'separate_modules': True,
     'exclude_patterns': ['../../vermouth/tests/*', '../../vermouth/redistributed/*']
     }
]

autodoc_inherit_docstrings = False
autoclass_content = 'both'
autodoc_default_options = {'members': None,
                           'undoc-members': None,
                           'show-inheritance': None}

napoleon_google_docstring = False
napoleon_numpy_docstring = True
napoleon_preprocess_types = False
napoleon_use_param = True
napoleon_type_aliases = {
        'Molecule': 'vermouth.molecule.Molecule',
        }
# -- Options for intersphinx extension ---------------------------------------
# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {
    'python': ('https://docs.python.org/3', None),
    'networkx': ('https://networkx.org/documentation/latest', None),
    'numpy': ('https://numpy.org/doc/stable', None),
    'scipy': ('https://docs.scipy.org/doc/scipy', None),
}


# Borrowed from https://github.com/sphinx-doc/sphinx/issues/5603
# On top of that, networkx.isomorphism.GraphMatcher is not documented, so link
# to the VF2 isomorphism module instead.
# See https://github.com/networkx/networkx/issues/3239
intersphinx_aliases = {
    #('py:class', 'networkx.classes.graph.Graph'): ('py:class', 'networkx.Graph'),
    #('py:class', 'networkx.algorithms.isomorphism.vf2userfunc.GraphMatcher'): ('py:class', 'networkx.isomorphism.GraphMatcher'),
    #('py:class', 'networkx.algorithms.isomorphism.vf2userfunc.GraphMatcher'): ('py:module','networkx.algorithms.isomorphism.isomorphvf2'),
    ('py:class', 'networkx.isomorphism.GraphMatcher'): ('py:module', 'networkx.algorithms.isomorphism.isomorphvf2')
}

autosectionlabel_prefix_document = True

def add_intersphinx_aliases_to_inv(app):
    from sphinx.ext.intersphinx import InventoryAdapter
    inventories = InventoryAdapter(app.builder.env)

    for alias, target in app.config.intersphinx_aliases.items():
        alias_domain, alias_name = alias
        target_domain, target_name = target
        try:
            found = inventories.main_inventory[target_domain][target_name]
            try:
                inventories.main_inventory[alias_domain][alias_name] = found
            except KeyError:
                continue
        except KeyError:
            continue


def setup(app):
    app.add_config_value('intersphinx_aliases', {}, 'env')
    app.connect('builder-inited', add_intersphinx_aliases_to_inv)
